Adsorption and Hybridization of Oligonucleotides on Mercaptoacetic Acid-Capped CdSe/ZnS Quantum Dots and Quantum Dot−Oligonucleotide Conjugates

Algar, W. Russ; Krull, Ulrich J.

doi:10.1021/la062217y

Cited by 105 publications

(107 citation statements)

References 39 publications

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“…To reduce the potential steric hinderances, the homopolymer of thymine sequence was employed. Compared with the mixed base sequence or a poly-A sequence, the homopolymer of thymine sequence showed no tendency to adsorb at neutral pH and a greater tendency to adsorb at basic pH (Algar and Krull 2006). Based on these work, TTTTTT was applied to keep the oligonucleotides away from the QDs in this study.…”

Section: Resultsmentioning

confidence: 98%

Fluorescence in situ hybridization (FISH) on maize metaphase chromosomes with quantum dot-labeled DNA conjugates

Huang

et al. 2007

Chromosoma

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Semiconductor nanocrystals, also called quantum dots (QDs), are novel inorganic fluorophores which are brighter and more photostable than organic fluorophores. In the present study, highly dispersive QD-labeled oligonucleotide (TAG)(8) (QD-deoxyribonucleic acid [DNA]) conjugates were constructed via the metal-thiol bond, which can be used as fluorescence in situ hybridization (FISH) probes. FISH analysis of maize metaphase chromosomes using the QD-DNA probes showed that the probes could penetrate maize chromosomes and nuclei and solely hybridized to complementary target DNAs. Compared with the conventional organic dyes such as Cy3 and fluorescein isothiocyanate, this class of luminescent labels bound with oligonucleotides is brighter and more stable against photobleaching on the chromosomes after FISH. These results suggest that QD fluorophores may be a more stable and useful fluorescent label for FISH applications in plant chromosome mapping considering their size-tunable luminescence spectra.

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Section: Resultsmentioning

confidence: 98%

Fluorescence in situ hybridization (FISH) on maize metaphase chromosomes with quantum dot-labeled DNA conjugates

Huang

et al. 2007

Chromosoma

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“…We have studied the adsorption of oligonucleotides on MAA-capped QDs using a series of FRET experiments [67]. By fluorescently labeling the oligonucleotide such that the absorption spectrum of the dye overlapped with the PL spectrum of the QD, it was possible to monitor the adsorption of oligonucleotides via FRET-sensitized dye fluorescence.…”

Section: Ligand Exchange and Biomoleculesmentioning

confidence: 99%

“…With respect to conjugated oligonucleotides, it was also possible to investigate the conformation of these oligonucleotides qualitatively via FRET [67]. By varying the acceptor dye position between the 3 0 and 5 0 termini and varying the length of linker between the QD and oligonucleotide, it was determined that the oligonucleotide adopted a conformation along the surface of the QD.…”

Section: Ligand Exchange and Biomoleculesmentioning

confidence: 99%

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Quantum Dots for the Development of Optical Biosensors Based on Fluorescence

Algar

Krull

2009

Biosensing Using Nanomaterials

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“…1,2 Adsorptive interactions between oligonucleotides and QDs have also been reported and rationalized in terms of a hydrogen-bonding model. Algar and Krull 10 showed that conjugated oligonucleotides adopt a conformation that lies along the surface of the QD. The formation of these coupled structures is supposed to reduce the donor-acceptor distance and to improve the FRET efficiency.…”

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confidence: 99%

Nuclease Tolerant FRET Probe Based on DNA-Quantum Dot Conjugation

et al. 2008

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Hybrid materials consisting of quantum dots (QDs) coupled to peptides, DNA and proteins are currently of great interest in the developing research area of nanobiotechnology. 1-7 QD-based FRET (fluorescence resonance energy transfer) probes have recently been reported, including QD-conjugated hybridization probes for the preliminary screening of siRNA sequences 8 and an ultrasensitive DNA nanosensor with a single quantum dot, which are benefited by the use of the unique photophysical properties of QDs and their conjugates.Actually, QDs are applied as an excellent donor in FRET due to their narrow emission and broad excitation spectra, enabling an effective separation of the donor and the acceptor fluorescence, and the selection of a wide range of excitation wavelengths to reduce the background. By placing both donor and acceptor fluorophores at precise locations on the molecule of interest, information on distance and angle changes between the two fluorophores, or conformational and structural changes of the labeled molecules can be extracted through FRET measurements. 10-13A more specific example of one type of measurement of current interest may be drawn from the current work of Ho et al.14 on the intracellular stability and unpacking of a DNA molecule. They used a QD-mediated FRET to determine the dynamic stability and the composition of plasmid DNA during intracellular transport, and achieved the precise detection of discrete changes in the nanocomplex state against various intracellular microenvironments. This approach provides a convenient method to follow the intra-or intercellular trafficking of DNA nanocomplexes over time. However, these nucleic acids are very susceptible to a nuclease attack under physiological conditions. 15 To overcome this problem, we have recently developed a unique FRET-inducing QD-DNA conjugate that is tolerant to nuclease digestion. Here, we report on a FRET analysis for structural changes of the QD-DNA conjugates and the inhibitory effect on the enzymatic reaction by dye binding.QD-DNA conjugates were prepared by varying the QD/DNA ratio (QD/DNA = 17, 168 and 1678) and using gel electrophoresis to separate the products. The method used for the conjugation of QD and DNA is schematically depicted in Fig. 1. 16 In brief, 3′-biotinylated 14-mer oligonucleotide (5′GGGCGGCGACCTAA3′-biotin, Sigma Genosys) was hybridized with complementary 5′-overhang (12 base) of λDNA (Takara Bio) and linked by ligation. The biotinylated λDNA (0.30, 3.0 and 30 pM) was reacted with streptavidin-coated CdSe/ZnS QD (0.5 nM, Qdot 605 Streptavidin Conjugate, Quantum Dot Corp.) in 82 mM NaHCO3 (pH 8.0). Each QD typically has 5 -10 streptavidins on its surface (User Manual PN 90-0003J Rev 9.1), thus providing several types of We have developed a fluorescence resonance energy transfer (FRET) probe based on the conjugation of a quantum dot (QD) with dye (YOYO-3) intercalated DNA. The FRET-inducing electrostatic coupling of DNA and the QD made structural changes to the QD-DNA conjugates, which significantly prev...

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Adsorption and Hybridization of Oligonucleotides on Mercaptoacetic Acid-Capped CdSe/ZnS Quantum Dots and Quantum Dot−Oligonucleotide Conjugates

Cited by 105 publications

References 39 publications

Fluorescence in situ hybridization (FISH) on maize metaphase chromosomes with quantum dot-labeled DNA conjugates

Fluorescence in situ hybridization (FISH) on maize metaphase chromosomes with quantum dot-labeled DNA conjugates

Quantum Dots for the Development of Optical Biosensors Based on Fluorescence

Nuclease Tolerant FRET Probe Based on DNA-Quantum Dot Conjugation

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